| 1 | In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer’s disease 2025, 2, | | 3 | Citations (PDF) |
| 2 | A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites | 6.0 | 11 | Citations (PDF) |
| 3 | Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism | 4.5 | 15 | Citations (PDF) |
| 4 | Microbial Abundances Retrieved from Sequencing data—automated NCBI Taxonomy (MARS): a pipeline to create relative microbial abundance data for the Microbiome Modelling Toolbox and utilizing homosynonyms for efficient mapping to resources | 2.4 | 4 | Citations (PDF) |
| 5 | Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases | 27.4 | 19 | Citations (PDF) |
| 6 | Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities | 10.3 | 15 | Citations (PDF) |
| 7 | Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome | 17.0 | 62 | Citations (PDF) |
| 8 | Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine | 32.5 | 224 | Citations (PDF) |
| 9 | A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models | 6.8 | 11 | Citations (PDF) |
| 10 | Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics | 10.3 | 29 | Citations (PDF) |
| 11 | Circulating metabolites modulated by diet are associated with depression | 8.5 | 41 | Citations (PDF) |
| 12 | The Effects of Hospitalisation on the Serum Metabolome in COVID-19 Patients | 3.5 | 5 | Citations (PDF) |
| 13 | Cardinality optimization in constraint-based modelling: application to human metabolism | 4.7 | 7 | Citations (PDF) |
| 14 | Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities | 4.7 | 49 | Citations (PDF) |
| 15 | NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health | 3.5 | 17 | Citations (PDF) |
| 16 | The gut microbial metabolite formate exacerbates colorectal cancer progression | 18.5 | 259 | Citations (PDF) |
| 17 | MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions | 4.7 | 6 | Citations (PDF) |
| 18 | An international classification of inherited metabolic disorders (<scp>ICIMD</scp>) | 3.2 | 293 | Citations (PDF) |
| 19 | Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of <i>Fusobacterium</i> spp. on community butyrate production | 10.3 | 33 | Citations (PDF) |
| 20 | Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism | 13.9 | 34 | Citations (PDF) |
| 21 | Methanogenic granule growth and development is a continual process characterized by distinct morphological features | 8.4 | 13 | Citations (PDF) |
| 22 | Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis | 3.0 | 87 | Citations (PDF) |
| 23 | Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes | 14.8 | 24 | Citations (PDF) |
| 24 | Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine | 9.3 | 67 | Citations (PDF) |
| 25 | Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism | 3.2 | 17 | Citations (PDF) |
| 26 | DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations | 4.7 | 28 | Citations (PDF) |
| 27 | Advances in constraint-based modelling of microbial communities | 1.4 | 51 | Citations (PDF) |
| 28 | Early-Life Adversity Leaves Its Imprint on the Oral Microbiome for More Than 20 Years and Is Associated with Long-Term Immune Changes | 4.5 | 22 | Citations (PDF) |
| 29 | Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease | 6.8 | 161 | Citations (PDF) |
| 30 | Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome | 7.0 | 197 | Citations (PDF) |
| 31 | Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions | 4.0 | 194 | Citations (PDF) |
| 32 | Predicting gastrointestinal drug effects using contextualized metabolic models | 3.2 | 20 | Citations (PDF) |
| 33 | Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome | 2.4 | 32 | Citations (PDF) |
| 34 | Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig | 3.5 | 20 | Citations (PDF) |
| 35 | Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development | 3.0 | 16 | Citations (PDF) |
| 36 | Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease | 11.5 | 312 | Citations (PDF) |
| 37 | Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells | 6.4 | 84 | Citations (PDF) |
| 38 | A blood-based signature of cerebrospinal fluid Aβ1–42 status | 3.5 | 25 | Citations (PDF) |
| 39 | Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 | 24.3 | 1,172 | Citations (PDF) |
| 40 | The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease | 15.8 | 379 | Citations (PDF) |
| 41 | The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities | 4.7 | 137 | Citations (PDF) |
| 42 | Recon3D enables a three-dimensional view of gene variation in human metabolism | 32.5 | 744 | Citations (PDF) |
| 43 | Modeling metabolism of the human gut microbiome | 7.0 | 132 | Citations (PDF) |
| 44 | From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease | 3.0 | 80 | Citations (PDF) |
| 45 | From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota | 4.5 | 85 | Citations (PDF) |
| 46 | Finding useful biomarkers for Parkinson’s disease | 13.4 | 150 | Citations (PDF) |
| 47 | ReconMap: an interactive visualization of human metabolism | 4.7 | 62 | Citations (PDF) |
| 48 | Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression | 3.5 | 36 | Citations (PDF) |
| 49 | DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia | 4.7 | 31 | Citations (PDF) |
| 50 | Quantitative systems pharmacology and the personalized drug–microbiota–diet axis | 1.4 | 42 | Citations (PDF) |
| 51 | Leigh map: A novel computational diagnostic resource for mitochondrial disease | 6.3 | 82 | Citations (PDF) |
| 52 | Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D | 5.5 | 32 | Citations (PDF) |
| 53 | Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides | 2.4 | 103 | Citations (PDF) |
| 54 | BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities | 3.2 | 256 | Citations (PDF) |
| 55 | A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines | 3.2 | 30 | Citations (PDF) |
| 56 | CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models | 4.7 | 85 | Citations (PDF) |
| 57 | Gut microbiota functions: metabolism of nutrients and other food components | 3.6 | 2,361 | Citations (PDF) |
| 58 | Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis | 3.9 | 60 | Citations (PDF) |
| 59 | MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models | 2.9 | 53 | Citations (PDF) |
| 60 | Metabolomics enables precision medicine: “A White Paper, Community Perspective” | 2.8 | 519 | Citations (PDF) |
| 61 | Conditions for duality between fluxes and concentrations in biochemical networks | 1.7 | 15 | Citations (PDF) |
| 62 | Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota | 32.5 | 802 | Citations (PDF) |
| 63 | Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients | 3.0 | 39 | Citations (PDF) |
| 64 | Systems biology of host–microbe metabolomics | 7.7 | 89 | Citations (PDF) |
| 65 | Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires | 11.5 | 47 | Citations (PDF) |
| 66 | Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes | 2.4 | 775 | Citations (PDF) |
| 67 | Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes
<i>In Silico</i> | 3.5 | 119 | Citations (PDF) |
| 68 | Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework | 10.3 | 107 | Citations (PDF) |
| 69 | Modeling the effects of commonly used drugs on human metabolism | 5.5 | 33 | Citations (PDF) |
| 70 | Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease | 2.9 | 89 | Citations (PDF) |
| 71 | Genome-Scale Methods Converge on Key Mitochondrial Genes for the Survival of Human Cardiomyocytes in Hypoxia | 3.8 | 8 | Citations (PDF) |
| 72 | <scp>fast</scp>G<scp>ap</scp>F<scp>ill</scp>: efficient gap filling in metabolic networks | 4.7 | 121 | Citations (PDF) |
| 73 | Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota | 3.9 | 53 | Citations (PDF) |
| 74 | Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 | 5.5 | 25 | Citations (PDF) |
| 75 | Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe | 2.9 | 224 | Citations (PDF) |
| 76 | Prediction of intracellular metabolic states from extracellular metabolomic data | 2.8 | 69 | Citations (PDF) |
| 77 | Applying systems biology methods to the study of human physiology in extreme environments | 2.0 | 27 | Citations (PDF) |
| 78 | Consensus and conflict cards for metabolic pathway databases | 3.2 | 13 | Citations (PDF) |
| 79 | A systems biology approach to studying the role of microbes in human health | 7.0 | 115 | Citations (PDF) |
| 80 | Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut | 10.3 | 231 | Citations (PDF) |
| 81 | A community-driven global reconstruction of human metabolism | 32.5 | 1,001 | Citations (PDF) |
| 82 | Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity | 3.9 | 24 | Citations (PDF) |
| 83 | Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells | 3.0 | 71 | Citations (PDF) |
| 84 | Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration | 1.7 | 8 | Citations (PDF) |
| 85 | Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis | 7.8 | 291 | Citations (PDF) |
| 86 | A compendium of inborn errors of metabolism mapped onto the human metabolic network | 3.2 | 73 | Citations (PDF) |
| 87 | An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production | 9.1 | 35 | Citations (PDF) |
| 88 | Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction | 2.2 | 53 | Citations (PDF) |
| 89 | Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage | 2.4 | 109 | Citations (PDF) |
| 90 | Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies | 2.6 | 47 | Citations (PDF) |
| 91 | A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm | 2.4 | 45 | Citations (PDF) |
| 92 | Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling | 2.4 | 5 | Citations (PDF) |
| 93 | A Systems Biology Approach to the Evolution of Codon Use Pattern | 0.1 | 2 | Citations (PDF) |
| 94 | The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions | 3.2 | 66 | Citations (PDF) |
| 95 | A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 | 3.2 | 137 | Citations (PDF) |
| 96 | von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models | 4.7 | 60 | Citations (PDF) |
| 97 | rBioNet: A COBRA toolbox extension for <i>r</i>econstructing high-quality <i>bio</i>chemical <i>net</i>works | 4.7 | 61 | Citations (PDF) |
| 98 | Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS) | 3.5 | 78 | Citations (PDF) |
| 99 | A systems biology approach for human metabolism in health and disease | 4.8 | 0 | Citations (PDF) |
| 100 | A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 | 3.2 | 153 | Citations (PDF) |
| 101 | Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism | 1.7 | 57 | Citations (PDF) |
| 102 | What is flux balance analysis? | 32.5 | 3,818 | Citations (PDF) |
| 103 | Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery | 2.2 | 61 | Citations (PDF) |
| 104 | Reconstruction annotation jamborees: a community approach to systems biology | 7.0 | 55 | Citations (PDF) |
| 105 | Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling | 3.2 | 53 | Citations (PDF) |
| 106 | Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization | 3.2 | 169 | Citations (PDF) |
| 107 | Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli | 2.1 | 78 | Citations (PDF) |
| 108 | Metabolic network analysis integrated with transcript verification for sequenced genomes | 26.1 | 87 | Citations (PDF) |
| 109 | Three-Dimensional Structural View of the Central Metabolic Network of
<i>Thermotoga maritima</i> | 37.0 | 188 | Citations (PDF) |
| 110 | A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory | 3.2 | 243 | Citations (PDF) |
| 111 | Reconstruction of biochemical networks in microorganisms | 86.4 | 831 | Citations (PDF) |
| 112 | Global reconstruction of the human metabolic network based on genomic and bibliomic data | 7.8 | 1,328 | Citations (PDF) |
| 113 | Estimation of the number of extreme pathways for metabolic networks | 3.0 | 44 | Citations (PDF) |
| 114 | Candidate States of Helicobacter pylori’s Genome-Scale Metabolic Network upon Application of “Loop Law” Thermodynamic Constraints | 2.2 | 46 | Citations (PDF) |
| 115 | Towards multidimensional genome annotation | 46.1 | 332 | Citations (PDF) |
| 116 | Expanded Metabolic Reconstruction of
Helicobacter pylori
(
i
IT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants | 2.9 | 231 | Citations (PDF) |
| 117 | Candidate Metabolic Network States in Human Mitochondria | 2.3 | 141 | Citations (PDF) |
| 118 | The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes | 15.8 | 1,944 | Citations (PDF) |
